Diff of the two buildlogs: -- --- b1/build.log 2025-09-02 11:21:06.430881366 +0000 +++ b2/build.log 2025-09-02 11:24:55.467141270 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 1 23:17:14 -12 2025 -I: pbuilder-time-stamp: 1756811834 +I: Current time: Tue Oct 6 07:44:08 +14 2026 +I: pbuilder-time-stamp: 1791222248 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ dpkg-source: info: applying fix_missing_cstring_riscv64.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3685110/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3489447/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 5 17:44 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3489447/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3489447/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3bbf90834e2444c2afffb6f147ab55cc' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3685110' - PS1='# ' - PS2='> ' + INVOCATION_ID=71208930b56f44dda2cdc6ab026b8102 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3489447 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ggEQfpG2/pbuilderrc_jTTd --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ggEQfpG2/b1 --logfile b1/build.log diamond-aligner_2.1.11-2.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ggEQfpG2/pbuilderrc_baWr --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ggEQfpG2/b2 --logfile b2/build.log diamond-aligner_2.1.11-2.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3685110/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3489447/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -173,7 +205,7 @@ Get: 58 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 32.3 MB in 1s (61.8 MB/s) +Fetched 32.3 MB in 0s (110 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19897 files and directories currently installed.) @@ -428,7 +460,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/diamond-aligner-2.1.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../diamond-aligner_2.1.11-2_source.changes +I: user script /srv/workspace/pbuilder/3489447/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/3489447/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/diamond-aligner-2.1.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../diamond-aligner_2.1.11-2_source.changes dpkg-buildpackage: info: source package diamond-aligner dpkg-buildpackage: info: source version 2.1.11-2 dpkg-buildpackage: info: source distribution unstable @@ -487,7 +523,7 @@ -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE --- Configuring done (6.2s) +-- Configuring done (1.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -504,7 +540,7 @@ -- Build files have been written to: /build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11' dh_auto_build - cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/diamond-aligner-2.1.11 -B/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -520,67 +556,67 @@ make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' cd /build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/diamond-aligner-2.1.11 /build/reproducible-path/diamond-aligner-2.1.11 /build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu/CMakeFiles/arch_avx2.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' +make -f CMakeFiles/arch_generic.dir/build.make CMakeFiles/arch_generic.dir/build make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' make -f CMakeFiles/arch_sse4_1.dir/build.make CMakeFiles/arch_sse4_1.dir/build make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' -make -f CMakeFiles/arch_generic.dir/build.make CMakeFiles/arch_generic.dir/build make -f CMakeFiles/arch_avx2.dir/build.make CMakeFiles/arch_avx2.dir/build make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' -[ 2%] Building CXX object CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -[ 2%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/search/stage1_2.cpp.o -[ 2%] Building CXX object CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o -[ 3%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -MF CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o.d -o CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/tools/benchmark.cpp -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/dp/swipe/swipe_wrapper.cpp -[ 4%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/anchored_wrapper.cpp.o -[ 4%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/masking/tantan.cpp.o -[ 6%] Building CXX object CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o -[ 6%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -[ 7%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -[ 7%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough 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'/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' +[ 14%] Built target arch_generic In function ‘typename __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:998:21, inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:1029:20, @@ -686,8 +724,6 @@ /usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 952 | *__first = __tmp; | ~~~~~~~~~^~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' -[ 14%] Built target 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Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -966,6 +1001,7 @@ /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/global_ranking/extend.cpp.o -MF CMakeFiles/diamond.dir/src/align/global_ranking/extend.cpp.o.d -o CMakeFiles/diamond.dir/src/align/global_ranking/extend.cpp.o -c 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.cpp.o -MF CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/blast/ncbi_std.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/lib/blast/ncbi_std.cpp -[ 92%] Building CXX object CMakeFiles/diamond.dir/src/util/tsv/table.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/table.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/table.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/table.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/util/tsv/table.cpp [ 93%] Building CXX object CMakeFiles/diamond.dir/src/util/tsv/file.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/file.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/file.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/file.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/util/tsv/file.cpp [ 93%] Building CXX object CMakeFiles/diamond.dir/src/util/tsv/record.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/util/tsv/record.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/record.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/record.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/util/tsv/record.cpp -[ 94%] Building CXX object CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/cluster/cascaded/wrapper.cpp -[ 95%] Building CXX object CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o +[ 94%] Building CXX object CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/cluster/cascaded/helpers.cpp +[ 95%] Building CXX object CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/cluster/cascaded/wrapper.cpp [ 95%] Building CXX object CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.11/src -I/build/reproducible-path/diamond-aligner-2.1.11/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o -MF CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o.d -o CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.11/src/output/daa/merge.cpp [ 96%] Building CXX object CMakeFiles/diamond.dir/src/chaining/backtrace.cpp.o @@ -1095,17 +1131,17 @@ make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.11' -cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games sh diamond-calls -+ mktemp -d -+ TESTDIR=/tmp/tmp.ZB2JCWFptH -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.ZB2JCWFptH/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path sh diamond-calls +++ mktemp -d ++ TESTDIR=/tmp/tmp.dznesENPSo ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.dznesENPSo/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -1118,7 +1154,7 @@ Building query histograms... [0.01s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.002s] Initializing temporary storage... [0s] Building reference histograms... [0.009s] Allocating buffers... [0s] @@ -1130,7 +1166,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1145,7 +1181,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1193,7 +1229,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1222,14 +1258,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.023s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1242,7 +1278,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1320,7 +1356,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1376,7 +1412,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1417,7 +1453,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1529,7 +1565,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1572,7 +1608,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.107s] +Computing alignments... [0.108s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -1582,17 +1618,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.651s +Total time = 0.771s Reported 77 pairwise alignments, 77 HSPs. 72 queries aligned. -+ diamond blastp --threads 1 --db test/E.faa.diamond --query test/C.faa --out /tmp/tmp.ZB2JCWFptH/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/E.faa.diamond --query test/C.faa --out /tmp/tmp.dznesENPSo/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -1674,7 +1710,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1687,7 +1723,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2010,7 +2046,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2069,17 +2105,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.56s +Total time = 0.562s Reported 41 pairwise alignments, 41 HSPs. 15 queries aligned. -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/L.faa --out /tmp/tmp.ZB2JCWFptH/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/L.faa --out /tmp/tmp.dznesENPSo/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -2160,7 +2196,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2216,7 +2252,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2251,7 +2287,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2546,27 +2582,27 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.048s] +Computing alignments... [0.243s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] Deallocating queries... [0s] Loading query sequences... [0s] Closing the input file... [0s] -Closing the output file... [0s] +Closing the output file... [0.069s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.484s +Total time = 0.738s Reported 64 pairwise alignments, 64 HSPs. 33 queries aligned. -+ diamond blastp --threads 1 --db test/L.faa.diamond --query test/C.faa --out /tmp/tmp.ZB2JCWFptH/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/L.faa.diamond --query test/C.faa --out /tmp/tmp.dznesENPSo/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -2580,7 +2616,7 @@ Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] -Initializing temporary storage... [0s] +Initializing temporary storage... [0.231s] Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -2620,7 +2656,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2676,7 +2712,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2732,7 +2768,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2788,14 +2824,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2956,14 +2992,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2984,14 +3020,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3012,14 +3048,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3033,27 +3069,27 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.089s] +Computing alignments... [0.22s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] Deallocating queries... [0s] Loading query sequences... [0s] Closing the input file... [0s] -Closing the output file... [0s] +Closing the output file... [0.026s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.511s +Total time = 1.096s Reported 133 pairwise alignments, 133 HSPs. 109 queries aligned. -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/M.faa --out /tmp/tmp.ZB2JCWFptH/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/M.faa --out /tmp/tmp.dznesENPSo/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -3067,7 +3103,7 @@ Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.003s] -Initializing temporary storage... [0.002s] +Initializing temporary storage... [0s] Building reference histograms... [0.009s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -3075,17 +3111,17 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3162,14 +3198,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3358,7 +3394,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3386,7 +3422,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3505,7 +3541,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3520,7 +3556,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.047s] +Computing alignments... [0.046s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3530,17 +3566,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.48s +Total time = 0.492s Reported 62 pairwise alignments, 62 HSPs. 33 queries aligned. -+ diamond blastp --threads 1 --db test/M.faa.diamond --query test/C.faa --out /tmp/tmp.ZB2JCWFptH/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/M.faa.diamond --query test/C.faa --out /tmp/tmp.dznesENPSo/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -3554,7 +3590,7 @@ Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] -Initializing temporary storage... [0.001s] +Initializing temporary storage... [0.099s] Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -3569,7 +3605,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -3601,7 +3637,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3797,7 +3833,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3909,7 +3945,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3950,15 +3986,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.019s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4007,27 +4043,27 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.086s] +Computing alignments... [0.085s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] Deallocating queries... [0s] Loading query sequences... [0s] Closing the input file... [0s] -Closing the output file... [0s] +Closing the output file... [0.078s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.525s +Total time = 0.725s Reported 131 pairwise alignments, 131 HSPs. 109 queries aligned. -+ diamond blastp --ignore-warnings --threads 1 --db test/C.faa.diamond --query test/C2.faa --out /tmp/tmp.ZB2JCWFptH/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --ignore-warnings --threads 1 --db test/C.faa.diamond --query test/C2.faa --out /tmp/tmp.dznesENPSo/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -4041,7 +4077,7 @@ Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.003s] -Initializing temporary storage... [0.001s] +Initializing temporary storage... [0.068s] Building reference histograms... [0.009s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -4052,7 +4088,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4332,7 +4368,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4494,7 +4530,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.105s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4504,17 +4540,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.342s +Total time = 0.515s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/C.faa --out /tmp/tmp.ZB2JCWFptH/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/C.faa --out /tmp/tmp.dznesENPSo/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -4528,7 +4564,7 @@ Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] -Initializing temporary storage... [0s] +Initializing temporary storage... [0.161s] Building reference histograms... [0s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -4764,14 +4800,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4827,7 +4863,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4981,7 +5017,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.003s] +Computing alignments... [0.006s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4991,17 +5027,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.341s +Total time = 0.508s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/E.faa.diamond --query test/L.faa --out /tmp/tmp.ZB2JCWFptH/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/E.faa.diamond --query test/L.faa --out /tmp/tmp.dznesENPSo/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -5187,7 +5223,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5429,10 +5465,10 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5468,7 +5504,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.124s] +Computing alignments... [0.123s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5478,17 +5514,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.593s +Total time = 0.587s Reported 489 pairwise alignments, 489 HSPs. 32 queries aligned. -+ diamond blastp --threads 1 --db test/L.faa.diamond --query test/E.faa --out /tmp/tmp.ZB2JCWFptH/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/L.faa.diamond --query test/E.faa --out /tmp/tmp.dznesENPSo/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -5502,7 +5538,7 @@ Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] -Initializing temporary storage... [0.001s] +Initializing temporary storage... [0s] Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -5535,7 +5571,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5647,7 +5683,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5927,7 +5963,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5955,27 +5991,27 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.246s] +Computing alignments... [0.447s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] Deallocating queries... [0s] Loading query sequences... [0s] Closing the input file... [0s] -Closing the output file... [0s] +Closing the output file... [0.13s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.714s +Total time = 1.04s Reported 1173 pairwise alignments, 1173 HSPs. 72 queries aligned. -+ diamond blastp --threads 1 --db test/E.faa.diamond --query test/M.faa --out /tmp/tmp.ZB2JCWFptH/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/E.faa.diamond --query test/M.faa --out /tmp/tmp.dznesENPSo/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -5983,7 +6019,7 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.001s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] @@ -6070,7 +6106,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6291,7 +6327,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -6442,27 +6478,27 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.127s] +Computing alignments... [0.124s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] Deallocating queries... [0s] Loading query sequences... [0s] Closing the input file... [0s] -Closing the output file... [0s] +Closing the output file... [0.087s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.59s +Total time = 0.676s Reported 489 pairwise alignments, 489 HSPs. 32 queries aligned. -+ diamond blastp --threads 1 --db test/M.faa.diamond --query test/E.faa --out /tmp/tmp.ZB2JCWFptH/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/M.faa.diamond --query test/E.faa --out /tmp/tmp.dznesENPSo/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -6530,7 +6566,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6579,7 +6615,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6775,7 +6811,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.004s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6901,7 +6937,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6929,27 +6965,27 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.264s] +Computing alignments... [0.263s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] Deallocating queries... [0s] Loading query sequences... [0s] Closing the input file... [0s] -Closing the output file... [0s] +Closing the output file... [0.204s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.742s +Total time = 1.119s Reported 1173 pairwise alignments, 1173 HSPs. 72 queries aligned. -+ diamond blastp --ignore-warnings --threads 1 --db test/E.faa.diamond --query test/C2.faa --out /tmp/tmp.ZB2JCWFptH/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --ignore-warnings --threads 1 --db test/E.faa.diamond --query test/C2.faa --out /tmp/tmp.dznesENPSo/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -6967,7 +7003,7 @@ Building reference histograms... [0.01s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7416,7 +7452,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.122s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7426,17 +7462,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.361s +Total time = 0.476s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/E.faa --out /tmp/tmp.ZB2JCWFptH/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/E.faa --out /tmp/tmp.dznesENPSo/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -7450,15 +7486,15 @@ Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] -Initializing temporary storage... [0s] +Initializing temporary storage... [0.296s] Building reference histograms... [0s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0s] @@ -7756,7 +7792,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7903,7 +7939,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.17s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7913,17 +7949,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.347s +Total time = 0.816s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/L.faa.diamond --query test/M.faa --out /tmp/tmp.ZB2JCWFptH/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/L.faa.diamond --query test/M.faa --out /tmp/tmp.dznesENPSo/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -7931,7 +7967,7 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0.002s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] @@ -8390,27 +8426,27 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.09s] +Computing alignments... [0.222s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] Deallocating queries... [0s] Loading query sequences... [0s] Closing the input file... [0s] -Closing the output file... [0s] +Closing the output file... [0.068s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.603s +Total time = 0.798s Reported 390 pairwise alignments, 390 HSPs. 39 queries aligned. -+ diamond blastp --threads 1 --db test/M.faa.diamond --query test/L.faa --out /tmp/tmp.ZB2JCWFptH/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/M.faa.diamond --query test/L.faa --out /tmp/tmp.dznesENPSo/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -8418,7 +8454,7 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0.002s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] @@ -8877,27 +8913,27 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.094s] +Computing alignments... [0.246s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] Deallocating queries... [0s] Loading query sequences... [0s] Closing the input file... [0s] -Closing the output file... [0s] +Closing the output file... [0.05s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.591s +Total time = 0.924s Reported 390 pairwise alignments, 390 HSPs. 40 queries aligned. -+ diamond blastp --ignore-warnings --threads 1 --db test/L.faa.diamond --query test/C2.faa --out /tmp/tmp.ZB2JCWFptH/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --ignore-warnings --threads 1 --db test/L.faa.diamond --query test/C2.faa --out /tmp/tmp.dznesENPSo/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -8911,7 +8947,7 @@ Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.001s] -Initializing temporary storage... [0s] +Initializing temporary storage... [0.166s] Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -9125,7 +9161,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9364,7 +9400,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.003s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9374,17 +9410,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.262s +Total time = 0.567s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/L.faa --out /tmp/tmp.ZB2JCWFptH/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/L.faa --out /tmp/tmp.dznesENPSo/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -9392,7 +9428,7 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0.002s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] @@ -9822,7 +9858,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9851,7 +9887,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.249s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9861,17 +9897,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.252s +Total time = 0.507s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --ignore-warnings --threads 1 --db test/M.faa.diamond --query test/C2.faa --out /tmp/tmp.ZB2JCWFptH/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --ignore-warnings --threads 1 --db test/M.faa.diamond --query test/C2.faa --out /tmp/tmp.dznesENPSo/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -9893,14 +9929,14 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -10141,7 +10177,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10338,7 +10374,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.08s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10348,17 +10384,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.247s +Total time = 0.331s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/M.faa --out /tmp/tmp.ZB2JCWFptH/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/M.faa --out /tmp/tmp.dznesENPSo/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.11.165 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.ZB2JCWFptH +Temporary directory: /tmp/tmp.dznesENPSo #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -10366,13 +10402,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0.002s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] -Initializing temporary storage... [0s] +Initializing temporary storage... [0.217s] Building reference histograms... [0s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -10835,15 +10871,15 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.244s +Total time = 0.482s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ rm -rf /tmp/tmp.ZB2JCWFptH ++ rm -rf /tmp/tmp.dznesENPSo make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.11' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/diamond-aligner/ - cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/diamond-aligner-2.1.11/debian/diamond-aligner AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/diamond-aligner-2.1.11/debian/diamond-aligner AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/diamond-aligner-2.1.11 -B/build/reproducible-path/diamond-aligner-2.1.11/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -10884,12 +10920,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3489447/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3489447/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3685110 and its subdirectories -I: Current time: Mon Sep 1 23:21:06 -12 2025 -I: pbuilder-time-stamp: 1756812066 +I: removing directory /srv/workspace/pbuilder/3489447 and its subdirectories +I: Current time: Tue Oct 6 07:47:55 +14 2026 +I: pbuilder-time-stamp: 1791222475